Heroes of EVA: Filling in the Blanks
by eastWOLF
Summary: Misato was the only survivor of the Katsuragi Expedition that awoke Adam, the cause of Second Impact. Her mind was destroyed and now it has to be rebuilt along with her perception of this new world. Crossover with Marvel, DC Universe, Image & Dark Horse!
1. Destroyed

Heroes of EVA: Filling in the Blanks

**Disclaimer: Neon Genesis Evangelion and all Marvel, DC Universe, Image, and Dark Horse properties belong to their respected owners.**

**Author's Note: Well it's another side and this time it's about my favorite character Misato! I did this one because a few people have asked me why doesn't Misato have powers in the beginning of 'The Ties That Bind' since she was right there when Second Impact happened. Well this gives an answer to that.**

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><p><span>Chapter 1: Destroyed<span>

_I wish I had normal life, but my life is far from it. I wished my dad would notice me and that my mom didn't cry, but those wishes never came true. We had superheroes when I was little and I would always think where's Superman when mom and dad are fighting? Where's Wonder Woman when I would get hurt? I was always ignored and I wasn't special…well that was until Second Impact happened. _

_-Misato Katsuragi_

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><p><span>September 12, 2000: Antarctica:<span>

"I'd like you to come with me on my Expedition to Antarctica" were the words that replayed over and over in young Misato's mind. Her father Ryota Katsuragi was the head scientist of his self-titled Expedition that was used to research a "being" uncovered in the South Pole. Misato really didn't care for all that science mumbo-jumbo and knew the only reason why she was there because this was her father's feeble way of convincing her that he loved her.

'_Yeah right.' _the purple haired fourteen year sighed. _'He's only interested in his work.'_ She looked over from her seat in the corner to see her father doing just that. _'He never pays attention to me or mom.' _Misato now recalling how her father always caused her mother pain and force her to cry herself asleep. She glanced at her father one last time before getting up and leaving the research tent. "I hate you father." She grumbled under her breather as she pulled her hood of her head protecting it from the harsh cold. "Why'd you have to take me on this stupid trip anyh-" her rant was cut short when she bumped into somebody.

"I'm sorry," she quickly started to apologize and looked up the person. "Ikari-san. I didn't see where I was going."

Gendo Ikari glared at the child but did acknowledge her. "It's alright, now if you'll excuse me…"

Misato noticed Gendo was carrying a suitcase and raised an eyebrow. "Are you leaving Ikari-san?"

"Yes, I've business back in Japan... I must regret I will not be able to witness the results of the Contact Experiment...but I will hope for good results..." he answered.

"Oh...Should I tell Father you're leaving?" she asked realizing it was at least something for her to do.

"If you must." He huffed out as he walked past the teen.

'_He's pretty creepy.' _Misato thought as she went back to the research tent.

Her father was the only one in the tent now and was on his cell phone. "...I understand Sir...but still... I'm confident that my theory is correct..."

Misato stepped forward. "...Father?"

"...Excuse me...but we'll have to continue this conversation at another time..." Dr. Katsuragi says as he ends his call. He sighed as if bored by his daughter and stressed at the same time. "What is it Misato?"

"...Ikari-san said he had business back in Japan...so he's going to be taking the transport out—"

"Yes, I know." Her father interrupted.

"So he told you?"

"...Well...in a way that only grown-ups could understand."

"Oh wel-" Misato was cut short again.

"If that's all you came here to tell me, would you please leave to my work and go somewhere?"

The teen lowered her head at this statement before leaving the tent. As she walked in the snow tears started rolling down her cheeks. _'Why am I crying? He always does this, he just doesn't care. Not about me or mom!'_

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><p>A few hours had passed since her father told her to leave him alone but now she was back with him. He wanted Misato to be there during the contact experiment with the "being" but she could care less. They were in a control room that monitored everything inside the large crater where the "being" was. Scientists gather around the viewing window to watch the contact but Misato drifted off to the back of the lab.<p>

'_Once this is all over I can go back home with mo-'_ she didn't get to finish her thought as a huge flash of white light filled the room followed by a huge explosion.

The explosion was so powerful that it eradicated the entire lab and the whole base camp in one swoop. People died instantly with blood spewing everywhere, organs being mashed and barely any survivors.

Misato was one of them, she was flung into a pile of dead bodies with her head covered in blood and part of her jacket ripped in the middle. She was broken and felt like dying right there the pain was so unbearable! She cried out in pain and fear as she heard her name being call out in the distance. She was disoriented fading in and out as a figured grabbed her. Things became less fuzzy and she saw her father covered in blood struggling to take her somewhere. "D-dad..?" she barely got out.

Ryota continued to struggle to get his daughter to safety. "M-Misato…stay with…me…please." The blood lose was getting to him as he spotted an emergency safety capsule.

For a minute Misato continued to fade until her father put her in the capsule. She stared at him as he took off his cross pendent and put it around her neck. She then heard him his final words. "I love you Misato." Before closing the capsule and falling to the ground in a bloody heap. Misato looked up one more time to see the things nightmares were made out of. All of her fears coming to life as she saw four orange demonic Angel wings in the sky. After that there was another cataclysmic blast that shattered part of the protective glass on the capsule and killed 3 million people in its wake. This was known as Second Impact.

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><p><strong>Author's Note: A short chapter yes but this is sort of my take on the last moments Misato has with her father and the beginning of Second Impact. Other than that check out my other Heroes of EVA stories and don't forget to review. Until next time.<strong>

**-eastWOLF**


	2. Silence

Chapter 2: Silence

"_It has been four days since the event dubbed Second Impact has ravaged the earth."_ Said a reporter for channel 2.

"_The body count continues to rise as rescue teams still search for survivors in various countries." _Said the reporter for channel 4.

"_So far 890 million people are reported dead with over 10 million still reported missing." _Said the reporter for channel 5.

"_At this time we still don't know the exact cause of Second Impact but some have speculated it was a meteorite that hit the South Pole."_ The channel 7 reporter said.

These were the reports that played all around the world, broadcasted in many different languages but at the moment that didn't matter to one group of people. In a darkly lit bunker that somehow survived Second Impact located in Japan two men and one woman sat at a large table. The video feed of all the reports were cut off and replaced with the words SEELE 01 SOUND ONLY in bold red letters.

"Gentlemen, Doctor," SEELE 01 started. "As you know Second Impact has happened…but not in the way that we intended."

"Yes," agreed Gendo Ikari. "Katsuragi has failed us the Illuminati and awoke the first Angel, Adam."

"Just like the Dead Sea Scrolls predicted." Stated the brunette female doctor named Naoko Akagi.

"Adam is the first of many," Commented an older man by the name of Kozo Fuyutsuki. "And with the destruction of nearly half the earth's population done by one Angel what will happen when the next one appears?"

Naoko looked at the man. "According to the scrolls the next Angel won't appear for ten more years."

"The scrolls also suggest the next Angel will appear in less than five Doctor." He shot back.

"No matter the case we will be ready for their arrival." Said SEELE 01.

"How?" questioned Fuyutsuki.

"With our latest invention known as Evangelion." SEELE 01 answered.

"Evangelion?" Fuyutsuki repeated.

"Yes, right now it is in the planning stages but I have high hopes as Doctor Akagi spearheads the project." Said the man hidden behind text.

"Yes Sir." Responded the scientist.

"As for you Ikari I am appointing you Commander of GEHIRN in the wake of this…disaster." Said SEELE 01.

"Understood Sir." Gendo said.

"Good, now in the meantime this meeting of the Illuminati is adjured." The feed of SEELE 01 ended leaving the other three in silence.

Gendo was the first to break that and turned to the older man. "Sensei as of right now I'd like to appoint you my second in command."

"Alright Ikari." Kozo agreed.

"Good, now as my first act as Commander there is a…side project I want the two of you to partake in."

The doctor and new vice commander both raised an eyebrow. "What do you have in mind?"

Gendo smirked evilly as he had a dangerous glint in his shaded eyes.

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><p>In the four days after Second Impact Misato had witnessed Hell on earth. After the first day she was rescued by a search team that found her escape capsule floating adrift in what was left of the Arctic Ocean, she was then taken back to Japan to get better medical treatment. By the second day she had awoken from her unconsciousness but was still in tremendous pain. By the third day the pain was eased as doctors put her pain relieving medicine. All of those days she didn't talk or move and on the fourth day it was no different. Misato was put on a stretcher and was being moved to a lab to be examined again. Her body was catatonic with her eyes staring blankly above. As she was being pushed through the halls of the medical ward people couldn't help but look on in horror.<p>

Comments like "poor kid" or "she's the only survivor" were heard constantly and who could blame them? The girl witnessed something she never was supposed to and saw her father die right before her eyes. Once in the lab Misato was put on an operating table and was then observed by a whole team of doctors.

In another room Gendo and Fuyutsuki watched on with the head doctor.

"What is the status of the child?" Gendo asked the doctor.

"Well Sir from what we know her condition is horrible and her psyche is...well…broken."

"Broken?" Questioned Fuyutsuki.

"Y-yes, Sir...broken." the doctor got out. "We feel she's lost her mind, most likely due to the Hell she witnessed."

"Of course, the Contact experiment failed. Adam awoke and as a result we've lost the entire southern pole." Gendo added.

"What do you want us to do Sir?"

Gendo stared at the catatonic girl. "Nothing."

"Sir?"

"Doctor as of right now GEHIRN is taking custody of this child." Gendo stated firmly. "The patient clearly has been traumatized but because her father was personally involved our organization will take care of her."

There was no room for discussion and the doctor had to agree. "Yes Sir I understand." He then walked away to tell the others.

As the two other men stayed behind Fuyutsuki spoke up. "Are you sure about this Ikari?"

"Yes sensei," Gendo nodded. "She is a liability, we can't let the truth be revealed."

"She is still so young and to be honest I don't think she will want to remember this."

"That is exactly why we're doing this…and in a way we are doing her a favor."

"Fine." Fuyutsuki sighed realizing his student's stubbornness. "But Yui is not going to be pleased with you."

Gendo smirked. "She'll never know."

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><p><strong>Author's Note: Yeah it's another short chapter but these aren't intended to be like that. For now this is all I got but find out what happens to Misato when Gendo takes over her mind reconstruction. So until next time.<strong>

**-eastWOLF**


	3. Rebuild

Chapter 3: Rebuild

"_It has been three weeks since Second Impact and while we still don't know the cause of this event we do know the outcome." _Said the reporter for channel 2.

"_Mutants walk among us." _Says the channel 4 news reporter.

"_Sources say that people are mutating and gaining extraordinary abilities," _fears the channel 5 reporter. _"Some so dangerous that they can kill an average person at will."_

"_There are over 100 known mutants in America alone." _Read out the channel 7 reporter. _"Most being teenagers and children as young as eight."_

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><p>Doctor Naoko Akagi was readying a hypodermic about to take blood from her patient. She looked behind her to see the catatonic body of fourteen year old Misato Katsuragi. Going up to the girl she grimaced. <em>'I've spent more time with this girl than my own daughter. Then again this girl can compromise everything we've worked for.'<em> Doctor Akagi drew blood from the girl's right arm before taking it to the medical lab.

For hours the doctor studied the blood sample trying to find something that was not there. _'How is this possible?' _she questioned almost wanting to pull her hair out. _'The child was right there at ground zero, she shoul-'_

Her thought were interrupted when the lab door opened up and Gendo Ikari walked in. "Doctor, progress report."

"Well Sir I haven't found any type of mutation within the child." Naoko told him. "Her blood is normal even after being exposed to Adam's blast at point blank range."

"No matter." Gendo said in a gruff tone. "If there is a mutation it will show its' self soon enough. In the meantime we can begin the mind reconstruction process. The sooner the better." He looked at Misato before turning to leave. "Oh and Doctor, I expect to see you at the usual spot by 9pm."

"Yes Sir." She sighed knowing full well what that meant. Gendo was pissed and needed to relieve stress on the person he was having an affair with. Yes he was just recently married but she couldn't argue because what Gendo wants Gendo gets. Naoko got back to her work trying not to think of the inevitable.

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><p><span>One Week Later:<span>

"How long before the procedure starts?" Gendo asked as he walked up to Fuyutsuki who was staring through a viewing window to the lab.

"We're almost ready to begin." The older man looked at his former pupil. "But is this all really necessary Ikari? Doctor Akagi's reports state that the child does not possess the mutation." _'But then again it is almost near to impossible to recognize it in its early stages.' _He added mentally.

"We can't be too sure sensei." Gendo said never taking his eyes off the viewing window. He pressed a button activating the intercom down in the lab. "Doctor are we ready?"

"Yes Sir," Naoko said in the lab. "We can begin." She looked to one of the lab technicians who was holding a very advanced piece of machinery. It was a helmet that had wires coming out of the top of it and connecting to various computers. "Apply the mind regenerator to the patient."

As the lab tech did as he was told the two commanders watched. "It's amazing; in only a month we still have access to this type of technology." Fuyutsuki noted.

"Yes, but then again with the money that SEELE is funding us money is no object." Gendo responded.

Back in the lab the mind regenerator helmet was placed on Misato's head and she was strapped to a metal gurney just in case she became violent in the process. Doctor Akagi was at the main work station and nodded to the lab techs. "Begin stage 1 of mind reconstruction now." All the technicians did as they were told and activated the device.

Misato laid there as the helmet came to life and flashed images of Second Impact repeatedly. At first the fourteen year old had no context for these images but then remembered everything. Though still catatonic she was afraid, very, very afraid and to show it she screamed in terror! "!"

"I think we just broke her out of her catatonic state." Gendo smirked coyly.

"Or reintroduced it," Fuyutsuki shot back. "Look the machine is hurting her!"

"!" Misato screamed as her nightmares came back to haunt her without even being asleep. Not only was she in physical pain but even more mental pain, tears started rolling down her cheeks and past the helmet's visors.

Gendo noticed this but did not care in the slightest he called down to the lab. "Doctor raise the power."

"Yes Sir." Akagi did as she was told without hesitation.

"What are you doing Ikari?" Fuyutsuki blared.

"Making sure the procedure works." Gendo said calmly. "The higher the power the better the outcome, simple as that."

"What?" the Vice Commander questioned. "You're insane!"

"Probably," Gendo agreed. "But it will be worth it."

Fuyutsuki looked from the screaming girl and then back to his former student. He had enough; yes he was working for the Illuminati but it wasn't worth seeing this innocent child being tortured. _'I'm risking everything here but I hope this works.'_ He stared straight into Gendo's eyes concentrating on his mind. _{Ikari you will stop this at once.}_

"I will stop this at once." Gendo repeated under some sort of trance. He turned on the intercom to the lab. "Doctor we are done for the day, end mind reconstruction program immediately."

"But Sir we're only at five percent complete with stage 1. This process could take days at a time." Doctor Akagi protested.

"I don't care if it takes months," Ikari said still under Fuyutsuki's apparent mind control. "I said end the program."

"Yes Sir." Akagi said with a hint of anger, when it came to science she didn't like to be told when to end an experiment.

_{Good Ikari, now tell them to release the girl.} _Fuyutsuki demanded.

"Take the girl back to the observation room." Gendo order the staff.

Two technicians unstrapped Misato as she continued to cry and not able to do anything else. They put her in a wheel chair and took her to the observation room with Doctor Akagi following behind them.

_{Now go to your office.} _After a while Fuyutsuki released his hold on Gendo's mind leaving him confused. On the other hand Fuyutsuki himself felt pretty drained of energy. _'Why am I not surprised?' _he asked himself. _"It's been months since I had to use my powers to this extent.'_ He ignored the dizziness as he walked to the observation room to see Misato still crying in terror. _'It doesn't matter, this girl had to pay for our sins and I will try and ease the pain the best of my abilities.'_

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><p><strong>Author's Note: Yes Fuyutsuki has telepathic powers which I will elaborate more on in the next chapter. Comments and reviews would be appreciated.<strong>

**-eastWOLF**


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